The bicentennial of the Gymnasium Museum (which existed as an independent institution in 1814–1939) calls for an analysis on the topic of science and museums in the modern era. Sources of information include library catalogues and infrequent reports about collections, which were mostly destroyed by 1945. The paper focuses on a selection of examples of scientific activities (particularly geology, palaeontology, and the social sciences) which were developed in relation to the Gymnasium Museum in the region of Czech Silesia. Unlike the Joanneum in Graz or the Brno museum, in which history held the dominant position, Opava was the backdrop for the thriving of natural sciences, particularly geognosy; i.e. geology, entomology, and botany. Since the collections are no longer intact, the intellectual settings have been reconstructed from the layout of the library. The same library also reveals value preferences in the domain of social sciences.